[gmx-users] Proper 1-octanol box preparation

[Ondrej Kroutil]

Hi GMX users!
I prepared a box of 125 1-octanol molecules using genconf -f
octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate
this system in NPT ensemble to get proper density and nice cube box,
similar to octanol configuration that one can download from
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies.
But I always got something completely different. Some cluster of the
molecules at the bottom of the simulation box, far away from dense
cube configuration. You can see picture here:
https://picasaweb.google.com/okroutil/Science#5738216101659210130. I
tried different thermo- and barostats, different coupling times,
compressibility, first NVT then NPT equil., but with no success. I
also tried more "chaotic" initial configuration generated with genbox
-ci ...gro - nmol 125 -box 5 5 5, no success.
So my question is: is there some simulation protocol or some setting
(higher pressure at the beginning of equilibration?), any trick
suitable for this type of solvent? Till now I worked only with water
and surfaces, so this is new area for me...

Thank you very much for any answer and have a nice day!

Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian
University, Czech Republic)

P.S.: I used gaff ff and topologies downloaded from
http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT
eq. input:

integrator           =  md
dt                   =  0.002
nsteps               =  500000
comm_mode            =  linear
nstcomm              =  1000
nstxout              =  0
nstxtcout            =  100
nstvout              =  0
nstfout              =  0
nstlog               =  500
nstlist              =  10
ns_type              =  grid
rlist                =  1.4
coulombtype          =  PME
rcoulomb             =  1.4
rvdw                 =  1.4
constraints          =  none
constraint_algorithm =  lincs
;shake_tol           =  0.00001
lincs_iter           =  1
fourierspacing       =  0.1
pme_order               =  4
ewald_rtol              =  1e-5
ewald_geometry          =  3d
optimize_fft            =  yes
; Nose-Hoover temperature coupling
Tcoupl             =  berendsen
tau_t              =  1
tc_grps            =  system
ref_t              =  298.
; No Pressure
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.6e-5
ref_p               =  1.0
; OTHER
periodic_molecules  =  no
pbc                 =  xyz
gen_vel             = yes
gen_temp            = 298.15
gen_seed            = -1--


Ondřej Kroutil
        ,,              Faculty of Health and Social Studies
   ----"))'             University of South Bohemia
     OOO           Jirovcova 24, Ceske Budejovice
      OOO          The Czech Republic
        | OO         E-mail:  okroutil at gmail.com
>------    O         Mobile:  +420 736 537 190